Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 114 of 125
Found at i:35214014 original size:19 final size:18
Alignment explanation
Indices: 35213987--35214075 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 18
35213977 TTAAATGTTT
35213987 TTTTTATATATTTTATGA
1 TTTTTATATATTTTATGA
35214005 TTTATTATAT-TTTTAT-A
1 TTT-TTATATATTTTATGA
*
35214022 TATTTTATGA-ATTTTTATAA
1 T-TTTTAT-ATA-TTTTATGA
35214042 TTTTTATAT-TTTTCATGA
1 TTTTTATATATTTT-ATGA
35214060 GTTTTTATATAATTTT
1 -TTTTTATAT-ATTTT
35214076 TACATGTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 19
0.75 0.01 0.24
Matches are distributed among these distances:
17 10 0.17
18 16 0.27
19 27 0.46
20 2 0.03
21 4 0.07
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTTATATATTTTATGA
Found at i:35214035 original size:28 final size:27
Alignment explanation
Indices: 35213987--35214069 Score: 116
Period size: 27 Copynumber: 3.0 Consensus size: 27
35213977 TTAAATGTTT
35213987 TTTTTATATATTTTATG-ATTTATTATA
1 TTTTTATATATTTTATGAATTT-TTATA
35214014 TTTTTATATATTTTATGAATTTTTATAA
1 TTTTTATATATTTTATGAATTTTTAT-A
*
35214042 TTTTTATAT-TTTTCATGAGTTTTTATA
1 TTTTTATATATTTT-ATGAATTTTTATA
35214069 T
1 T
35214070 AATTTTTACA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
27 27 0.52
28 25 0.48
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (27 bp):
TTTTTATATATTTTATGAATTTTTATA
Found at i:35214054 original size:9 final size:9
Alignment explanation
Indices: 35213986--35214089 Score: 75
Period size: 9 Copynumber: 11.0 Consensus size: 9
35213976 TTTAAATGTT
35213986 TTTTTTATA
1 TTTTTTATA
*
35213995 TATTTTATGA
1 TTTTTTAT-A
*
35214005 TTTATTATA
1 TTTTTTATA
35214014 -TTTTTATA
1 TTTTTTATA
*
35214022 TATTTTATGA
1 TTTTTTAT-A
*
35214032 ATTTTTATA
1 TTTTTTATA
*
35214041 ATTTTTATA
1 TTTTTTATA
*
35214050 TTTTTCATGA
1 TTTTTTAT-A
35214060 GTTTTTATATA
1 -TTTTT-TATA
* *
35214071 ATTTTTACA
1 TTTTTTATA
35214080 TGTTTTTATA
1 T-TTTTTATA
35214090 GAAAACAGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
8 7 0.09
9 33 0.45
10 26 0.35
11 6 0.08
12 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (9 bp):
TTTTTTATA
Found at i:35214771 original size:17 final size:17
Alignment explanation
Indices: 35214749--35214781 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35214739 GTGTCCTTCA
35214749 TGACATTATTTATATAT
1 TGACATTATTTATATAT
*
35214766 TGACATTTTTTATATA
1 TGACATTATTTATATA
35214782 ATATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
TGACATTATTTATATAT
Found at i:35215000 original size:32 final size:33
Alignment explanation
Indices: 35214942--35215009 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
35214932 TATAAATTTT
* *
35214942 AAAAAATTAAATTAAATTTTTATTATT-TTTAA
1 AAAAAATCAAAATAAATTTTTATTATTATTTAA
35214974 AAAAAATCAAAATATAATTTTT-TTATTAATTTAA
1 AAAAAATCAAAATA-AATTTTTATTATT-ATTTAA
35215008 AA
1 AA
35215010 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.55
33 7 0.23
34 7 0.23
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
AAAAAATCAAAATAAATTTTTATTATTATTTAA
Found at i:35215386 original size:17 final size:18
Alignment explanation
Indices: 35215360--35215394 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35215350 AAAATTAAAA
35215360 ATATTATAAATT-TTTTT
1 ATATTATAAATTATTTTT
*
35215377 ATATTTTAAATTATTTTT
1 ATATTATAAATTATTTTT
35215395 TGATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTATAAATTATTTTT
Found at i:35215394 original size:20 final size:20
Alignment explanation
Indices: 35215369--35215407 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35215359 AATATTATAA
*
35215369 ATTTTTTTATATTTTAAATT
1 ATTTTTTGATATTTTAAATT
*
35215389 ATTTTTTGATTTTTTAAAT
1 ATTTTTTGATATTTTAAAT
35215408 ATTATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
ATTTTTTGATATTTTAAATT
Found at i:35215410 original size:19 final size:18
Alignment explanation
Indices: 35215360--35215424 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
35215350 AAAATTAAAA
*
35215360 ATATTATAAAT-TTTTTT
1 ATATTTTAAATATTTTTT
35215377 ATATTTTAAATTATTTTTT
1 ATATTTTAAA-TATTTTTT
* * *
35215396 GATTTTTTAAATATTATTA
1 -ATATTTTAAATATTTTTT
*
35215415 AAATTTTAAA
1 ATATTTTAAA
35215425 AAAATTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 9 0.23
18 9 0.23
19 12 0.31
20 9 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATATTTTAAATATTTTTT
Found at i:35215624 original size:75 final size:73
Alignment explanation
Indices: 35215475--35215630 Score: 183
Period size: 75 Copynumber: 2.1 Consensus size: 73
35215465 CACAAAATTA
* * *
35215475 ATTTTAGATAATTTAATAAACGATAAAAATTTAAAAATTAAAGACTAAATTTAAAAATTACATGT
1 ATTTTAGATAATTTAATAAACGATAAAAATTTAAAAATTAAAGAATAAA--TAAAAATGACAAGT
**
35215540 ATTTCTATTT
64 ATTAATATTT
35215550 ATTTTAGATAATTTAATAAACGATAAAAATTTAAAAATTAAAAGAGATAAA-AAATAATGA-AAG
1 ATTTTAGATAATTTAATAAACGATAAAAATTTAAAAATT-AAAGA-ATAAATAAA-AATGACAAG
35215613 -ATTAAAATATTT
63 TATT--AATATTT
35215625 ATTTTA
1 ATTTTA
35215631 TAAAGTCGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
73 3 0.04
74 5 0.07
75 54 0.76
76 5 0.07
77 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.37
Consensus pattern (73 bp):
ATTTTAGATAATTTAATAAACGATAAAAATTTAAAAATTAAAGAATAAATAAAAATGACAAGTAT
TAATATTT
Found at i:35219554 original size:14 final size:14
Alignment explanation
Indices: 35219537--35219564 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35219527 TTTTATTCGA
35219537 ATTTTTTGAATTTG
1 ATTTTTTGAATTTG
35219551 ATTTTTTGAATTTG
1 ATTTTTTGAATTTG
35219565 GGTTCTGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (14 bp):
ATTTTTTGAATTTG
Found at i:35219946 original size:15 final size:15
Alignment explanation
Indices: 35219926--35219954 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35219916 AGATAATAAG
35219926 CATAACTCATTTTTC
1 CATAACTCATTTTTC
35219941 CATAACTCATTTTT
1 CATAACTCATTTTT
35219955 GTAATTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
CATAACTCATTTTTC
Found at i:35223137 original size:19 final size:18
Alignment explanation
Indices: 35223115--35223160 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
35223105 TATTTAATTC
*
35223115 TTTATTTGGTTAAATTATT
1 TTTATTTGATTAAA-TATT
*
35223134 TTTATTCTAATTAAATATT
1 TTTATT-TGATTAAATATT
35223153 TTTATTTG
1 TTTATTTG
35223161 TGTCCCACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (18 bp):
TTTATTTGATTAAATATT
Found at i:35239069 original size:12 final size:12
Alignment explanation
Indices: 35239054--35239117 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
35239044 ATCGTCGTCG
*
35239054 TCCTCTTCAACT
1 TCCTCTTCTACT
35239066 TCCTCTTCTACT
1 TCCTCTTCTACT
** *
35239078 TCAACTTCTTCT
1 TCCTCTTCTACT
*
35239090 TCCACTTCTACT
1 TCCTCTTCTACT
*
35239102 TCCTCTTCCACT
1 TCCTCTTCTACT
35239114 TCCT
1 TCCT
35239118 GTAGTTGCAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.12, C:0.42, G:0.00, T:0.45
Consensus pattern (12 bp):
TCCTCTTCTACT
Found at i:35239081 original size:18 final size:18
Alignment explanation
Indices: 35239058--35239115 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
35239048 TCGTCGTCCT
*
35239058 CTTCAACTTCCTCTTCTA
1 CTTCAACTTCCTCTTCCA
*
35239076 CTTCAACTTCTTCTTCCA
1 CTTCAACTTCCTCTTCCA
*
35239094 CTTCTACTTCCTCTTCCA
1 CTTCAACTTCCTCTTCCA
35239112 CTTC
1 CTTC
35239116 CTGTAGTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (18 bp):
CTTCAACTTCCTCTTCCA
Found at i:35246222 original size:11 final size:12
Alignment explanation
Indices: 35246183--35246237 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
35246173 CATTTATGGT
*
35246183 TCGTTTATTAGC
1 TCGTTTATAAGC
35246195 TCGTTTATAAGC
1 TCGTTTATAAGC
35246207 TCGTTTA-AAGC
1 TCGTTTATAAGC
*
35246218 CCGTTTATAAGC
1 TCGTTTATAAGC
35246230 TCGTTTAT
1 TCGTTTAT
35246238 TAGACCCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (12 bp):
TCGTTTATAAGC
Found at i:35247370 original size:10 final size:10
Alignment explanation
Indices: 35247347--35247493 Score: 52
Period size: 10 Copynumber: 14.5 Consensus size: 10
35247337 TTAAAATATC
35247347 TAAAAATATATA
1 TAAAAA-AT-TA
35247359 TAAAAAATTA
1 TAAAAAATTA
*
35247369 TAGAAAA-T-
1 TAAAAAATTA
** *
35247377 TGCAAAATTG
1 TAAAAAATTA
* **
35247387 CAAAAAAAAA
1 TAAAAAATTA
*
35247397 TAGAAAATTA
1 TAAAAAATTA
*
35247407 TAAAAAGTATA
1 TAAAAAAT-TA
*
35247418 TATAAAATTA
1 TAAAAAATTA
*
35247428 TGAAAAA-TA
1 TAAAAAATTA
* *
35247437 TAACATATTA
1 TAAAAAATTA
35247447 T--AAAATTA
1 TAAAAAATTA
*
35247455 TAATAAAACTATT
1 TAA-AAAA-T-TA
*
35247468 TTAAAAATTA
1 TAAAAAATTA
*
35247478 CAAAAATATTA
1 TAAAAA-ATTA
35247489 TAAAA
1 TAAAA
35247494 CAAAATTGAA
Statistics
Matches: 95, Mismatches: 30, Indels: 21
0.65 0.21 0.14
Matches are distributed among these distances:
8 11 0.12
9 8 0.08
10 39 0.41
11 23 0.24
12 11 0.12
13 3 0.03
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:35251092 original size:19 final size:19
Alignment explanation
Indices: 35251056--35251096 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
35251046 CAACTAAGTT
*
35251056 TTTTATTTAGTTGGTTTTG
1 TTTTATTTAATTGGTTTTG
**
35251075 TTTTATTTAATTTTTTTTG
1 TTTTATTTAATTGGTTTTG
35251094 TTT
1 TTT
35251097 GTTTGGATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (19 bp):
TTTTATTTAATTGGTTTTG
Found at i:35251186 original size:24 final size:23
Alignment explanation
Indices: 35251139--35251202 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
35251129 CGAACGTTAA
35251139 ACGAACATTAAACGAACATATTC
1 ACGAACATTAAACGAACATATTC
*
35251162 ACGAACATATAAAC-AAGCATGTTC
1 ACGAACAT-TAAACGAA-CATATTC
* *
35251186 ACGAACGTTAAATGAAC
1 ACGAACATTAAACGAAC
35251203 GAGCACGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 15 0.43
24 20 0.57
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (23 bp):
ACGAACATTAAACGAACATATTC
Found at i:35256517 original size:14 final size:13
Alignment explanation
Indices: 35256494--35256537 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
35256484 TAAAGTCAAT
35256494 TAAATATTTAAACA
1 TAAATATTTAAA-A
*
35256508 TAAATTTTTAAAA
1 TAAATATTTAAAA
35256521 -AAATATTTAAATA
1 TAAATATTTAAA-A
35256534 TAAA
1 TAAA
35256538 ACGTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 10 0.38
13 2 0.08
14 14 0.54
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAATATTTAAAA
Found at i:35261392 original size:21 final size:21
Alignment explanation
Indices: 35261363--35261402 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35261353 ATCACTTGTT
35261363 AAAAAAATAAAATATATGAAC
1 AAAAAAATAAAATATATGAAC
* * *
35261384 AAAATAATAAGATTTATGA
1 AAAAAAATAAAATATATGA
35261403 GGACGGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (21 bp):
AAAAAAATAAAATATATGAAC
Found at i:35263982 original size:7 final size:8
Alignment explanation
Indices: 35263957--35263981 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35263947 CGAAAATCTC
35263957 TTCTTTTT
1 TTCTTTTT
35263965 TTCTTTTT
1 TTCTTTTT
35263973 TTCTTTTT
1 TTCTTTTT
35263981 T
1 T
35263982 CAGAAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:35264431 original size:23 final size:23
Alignment explanation
Indices: 35264401--35264447 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
35264391 AAACATTAAG
35264401 TAAAAAACAAATTACCAGACTGC
1 TAAAAAACAAATTACCAGACTGC
*
35264424 TAAAAAACAAATTACTAGACTGC
1 TAAAAAACAAATTACCAGACTGC
35264447 T
1 T
35264448 CTATTGTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (23 bp):
TAAAAAACAAATTACCAGACTGC
Found at i:35268582 original size:31 final size:31
Alignment explanation
Indices: 35268547--35268620 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
35268537 CTTAGTAGCC
*
35268547 CAATGACTCAAATAAAAACTTTTGAATAGTT
1 CAATGACTCAAATAAAAACTTTCGAATAGTT
* **
35268578 CAATGACTTAAATGGAAACTTTCGAATAGTT
1 CAATGACTCAAATAAAAACTTTCGAATAGTT
35268609 CAATGAC-CAAAT
1 CAATGACTCAAAT
35268621 TGTAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (31 bp):
CAATGACTCAAATAAAAACTTTCGAATAGTT
Found at i:35269831 original size:18 final size:18
Alignment explanation
Indices: 35269808--35269850 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35269798 TTTTCAGTTG
35269808 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
35269826 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
35269844 TAATTAA
1 TAATTAA
35269851 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:35278185 original size:19 final size:18
Alignment explanation
Indices: 35278143--35278185 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
35278133 GAAAAAATAA
*
35278143 ATTA-TTAAAATAATTTT
1 ATTATTTAAAATAATTAT
35278160 ATATATTTAAAATAAATTAT
1 AT-TATTTAAAAT-AATTAT
35278180 ATTATT
1 ATTATT
35278186 ATGAGGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 11 0.50
20 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATTTAAAATAATTAT
Found at i:35296673 original size:17 final size:19
Alignment explanation
Indices: 35296651--35296695 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
35296641 CTTGATCCTT
*
35296651 TTATTT-CTCACGCTT-TA
1 TTATTTGCTCACCCTTATA
*
35296668 TTATTTGGTCACCCTTATA
1 TTATTTGCTCACCCTTATA
35296687 TTATTTGCT
1 TTATTTGCT
35296696 AATGACAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 7 0.30
19 10 0.43
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.53
Consensus pattern (19 bp):
TTATTTGCTCACCCTTATA
Found at i:35300899 original size:6 final size:6
Alignment explanation
Indices: 35300884--35300923 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
35300874 AATTCTGGAG
*
35300884 ATTATA ATTATC ATTATC ATTATC ATTATC ATTATC ATTA
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTA
35300924 AAGTTTGCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTATC
Found at i:35302172 original size:15 final size:15
Alignment explanation
Indices: 35302152--35302199 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
35302142 GACCCCAGCA
35302152 AATAAAGAGCAATAT
1 AATAAAGAGCAATAT
*
35302167 AATAAATA--AATA-
1 AATAAAGAGCAATAT
*
35302179 ATTAAAGAGCAATAT
1 AATAAAGAGCAATAT
35302194 AATAAA
1 AATAAA
35302200 TACATAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 4 0.15
15 12 0.46
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.23
Consensus pattern (15 bp):
AATAAAGAGCAATAT
Found at i:35302192 original size:27 final size:27
Alignment explanation
Indices: 35302154--35302207 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
35302144 CCCCAGCAAA
35302154 TAAAGAGCAATATAATAAATAAATAAT
1 TAAAGAGCAATATAATAAATAAATAAT
*
35302181 TAAAGAGCAATATAATAAATACATAAT
1 TAAAGAGCAATATAATAAATAAATAAT
35302208 ATCCCATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.26
Consensus pattern (27 bp):
TAAAGAGCAATATAATAAATAAATAAT
Found at i:35309058 original size:1 final size:1
Alignment explanation
Indices: 35309054--35309079 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
35309044 AAAAGGCAAA
35309054 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
35309080 AATTGGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:35309338 original size:2 final size:2
Alignment explanation
Indices: 35309290--35309322 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35309280 TCTCTCCCTC
35309290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35309323 CAGTTGTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35314844 original size:20 final size:19
Alignment explanation
Indices: 35314770--35314849 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 19
35314760 TTTATTAAAC
35314770 ATATAAATATTT-AAAAAAT
1 ATATAAA-ATTTAAAAAAAT
** *
35314789 ATA-AAAATAGAAATAAAT
1 ATATAAAATTTAAAAAAAT
* * *
35314807 ACATAAAAGTTCATAAAAAT
1 ATATAAAA-TTTAAAAAAAT
35314827 ATATAAAATTTAGAAAAAAT
1 ATATAAAATTTA-AAAAAAT
35314847 ATA
1 ATA
35314850 ATTATAAAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
17 2 0.04
18 11 0.24
19 10 0.22
20 23 0.50
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.29
Consensus pattern (19 bp):
ATATAAAATTTAAAAAAAT
Found at i:35314850 original size:28 final size:28
Alignment explanation
Indices: 35314782--35314873 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
35314772 ATAAATATTT
*
35314782 AAAAAATATAAAAATAGAAATAAA--TAC
1 AAAAAATATAAAAATA-AAAAAAATTTAC
* * * *
35314809 ATAAAAGTTCATAAAAATATATAAAATTTAG
1 A-AAAA-AT-ATAAAAATAAAAAAAATTTAC
**
35314840 AAAAAATATAATTATAAAAAAAATTTAC
1 AAAAAATATAAAAATAAAAAAAATTTAC
35314868 AAAAAA
1 AAAAAA
35314874 AATATGATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
27 1 0.02
28 26 0.53
29 6 0.12
30 13 0.27
31 3 0.06
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAAAATATAAAAATAAAAAAAATTTAC
Found at i:35315433 original size:19 final size:19
Alignment explanation
Indices: 35315409--35315468 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
35315399 TGTCTTTTTT
*
35315409 TATTTTTTATTTTTTATAA
1 TATTTTTTAATTTTTATAA
*
35315428 TATTTTTAAATTTTTAT-A
1 TATTTTTTAATTTTTATAA
*
35315446 TATTATTTTGACTTTTTA-AA
1 TATT-TTTT-AATTTTTATAA
35315466 TAT
1 TAT
35315469 ATATATTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.15
19 18 0.53
20 11 0.32
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTAATTTTTATAA
Found at i:35315435 original size:18 final size:18
Alignment explanation
Indices: 35315412--35315468 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 18
35315402 CTTTTTTTAT
35315412 TTTTTATTTTTTATAATA
1 TTTTTATTTTTTATAATA
*
35315430 TTTTTAAATTTTTATATATTA
1 TTTTT--ATTTTT-TATAATA
* *
35315451 TTTTGACTTTTTA-AATA
1 TTTTTATTTTTTATAATA
35315468 T
1 T
35315469 ATATATTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 4 0.12
18 7 0.22
19 5 0.16
20 6 0.19
21 10 0.31
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTATTTTTTATAATA
Found at i:35315483 original size:22 final size:20
Alignment explanation
Indices: 35315419--35315488 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
35315409 TATTTTTTAT
35315419 TTTTTATAATATT-TTTA-AA
1 TTTTTA-AATATTATTTAGAA
* * *
35315438 TTTTTATATATTATTTTGAC
1 TTTTTAAATATTATTTAGAA
35315458 TTTTTAAATATATATATTAGAA
1 TTTTTAAATAT-TAT-TTAGAA
35315480 TTTTATAAA
1 TTTT-TAAA
35315489 AAAAATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 11 0.28
21 3 0.08
22 8 0.20
23 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTAAATATTATTTAGAA
Found at i:35315683 original size:16 final size:16
Alignment explanation
Indices: 35315664--35315696 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35315654 TATATTTTTA
*
35315664 TTTTT-ATTTTTATAT
1 TTTTTAATTTATATAT
35315679 TTTTTAATTTATATAT
1 TTTTTAATTTATATAT
35315695 TT
1 TT
35315697 AATGAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTAATTTATATAT
Found at i:35315688 original size:22 final size:22
Alignment explanation
Indices: 35315651--35315697 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
35315641 TTTCTAAATG
* *
35315651 TTATATATTTTTATTTTTATTT
1 TTATATATTTTTATTTATATAT
35315673 TTATAT-TTTTTAATTTATATAT
1 TTATATATTTTT-ATTTATATAT
35315695 TTA
1 TTA
35315698 ATGAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATATATTTTTATTTATATAT
Found at i:35315689 original size:20 final size:22
Alignment explanation
Indices: 35315651--35315690 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
35315641 TTTCTAAATG
*
35315651 TTATATATTTTTATTTTTATTT
1 TTATATATTTTTATATTTATTT
35315673 TTATAT-TTTTTA-ATTTAT
1 TTATATATTTTTATATTTAT
35315691 ATATTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATATATTTTTATATTTATTT
Found at i:35320511 original size:3 final size:3
Alignment explanation
Indices: 35320503--35320554 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
35320493 TATTATGTTA
*
35320503 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35320551 AAT A
1 AAT A
35320555 CCAACCAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35328825 original size:95 final size:95
Alignment explanation
Indices: 35328662--35328850 Score: 360
Period size: 95 Copynumber: 2.0 Consensus size: 95
35328652 TACTACTTCT
*
35328662 AATCTCAAACAAAGCTAAGATATCCATGTCATGCTCCCGACAATACTCCTTAATGAATCTACCAA
1 AATCTCAAACAAAGCTAAGATATCCATGTCATGCTCCCGACAACACTCCTTAATGAATCTACCAA
35328727 GACGAGGGTTTCCAGACCCCTTAAAAATTG
66 GACGAGGGTTTCCAGACCCCTTAAAAATTG
35328757 AATCTCAAACAAAGCTAAGATATCCATGTCATGCTCCCGACAACACTCCTTAATGAATCTACCAA
1 AATCTCAAACAAAGCTAAGATATCCATGTCATGCTCCCGACAACACTCCTTAATGAATCTACCAA
*
35328822 GACGAGGGTTTCTAGACCCCTTAAAAATT
66 GACGAGGGTTTCCAGACCCCTTAAAAATT
35328851 TCAATCAAAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.24
Consensus pattern (95 bp):
AATCTCAAACAAAGCTAAGATATCCATGTCATGCTCCCGACAACACTCCTTAATGAATCTACCAA
GACGAGGGTTTCCAGACCCCTTAAAAATTG
Found at i:35332735 original size:29 final size:31
Alignment explanation
Indices: 35332672--35332739 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 31
35332662 TTTAAGTTTT
35332672 TTAAAAGTTGGAGGAAAAAAAATTTAGATCTC
1 TTAAAAGTTGGA-GAAAAAAAATTTAGATCTC
*
35332704 TTAAAAGTTGGA-AAAAAAAATTTAGGTC-C
1 TTAAAAGTTGGAGAAAAAAAATTTAGATCTC
35332733 TTAAAAG
1 TTAAAAG
35332740 CTAAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 8 0.23
30 15 0.43
32 12 0.34
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (31 bp):
TTAAAAGTTGGAGAAAAAAAATTTAGATCTC
Found at i:35333786 original size:38 final size:38
Alignment explanation
Indices: 35333744--35333821 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
35333734 CCACCACATC
35333744 TTGTACGGCTATAATTCAATCATTTTGCAAATTTCATT
1 TTGTACGGCTATAATTCAATCATTTTGCAAATTTCATT
35333782 TTGTACGGCTATAATTCAATCATTTTGCAAATTTCATT
1 TTGTACGGCTATAATTCAATCATTTTGCAAATTTCATT
35333820 TT
1 TT
35333822 ATATTATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (38 bp):
TTGTACGGCTATAATTCAATCATTTTGCAAATTTCATT
Found at i:35334888 original size:12 final size:11
Alignment explanation
Indices: 35334868--35334902 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
35334858 ATGACCATCA
35334868 CCACCATCCAT
1 CCACCATCCAT
35334879 CCATCCATCCAT
1 CCA-CCATCCAT
35334891 CCACACATCCAT
1 CCAC-CATCCAT
35334903 TACATACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.29, C:0.51, G:0.00, T:0.20
Consensus pattern (11 bp):
CCACCATCCAT
Found at i:35340040 original size:74 final size:75
Alignment explanation
Indices: 35339955--35340106 Score: 279
Period size: 75 Copynumber: 2.0 Consensus size: 75
35339945 GGTAAGCAAC
*
35339955 TCTTTTTCTTTTAATTTACTTAAAATCTTTCT-TATGGTTTTATATGAGGCCAAGAGGGTGTTTT
1 TCTTTTTCTTTTAATTTAATTAAAATCTTTCTCTATGGTTTTATATGAGGCCAAGAGGGTGTTTT
35340019 TCCAGTGGCT
66 TCCAGTGGCT
*
35340029 TCTTTTTCTTTTAATTTAATTAAATTCTTTCTCTATGGTTTTATATGAGGCCAAGAGGGTGTTTT
1 TCTTTTTCTTTTAATTTAATTAAAATCTTTCTCTATGGTTTTATATGAGGCCAAGAGGGTGTTTT
35340094 TCCAGTGGCT
66 TCCAGTGGCT
35340104 TCT
1 TCT
35340107 GTATGTCTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 30 0.40
75 45 0.60
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (75 bp):
TCTTTTTCTTTTAATTTAATTAAAATCTTTCTCTATGGTTTTATATGAGGCCAAGAGGGTGTTTT
TCCAGTGGCT
Found at i:35342082 original size:13 final size:12
Alignment explanation
Indices: 35342059--35342121 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 12
35342049 TTAACATTTT
*
35342059 TTTTAAGAAGTG
1 TTTTAAAAAGTG
*
35342071 TTGTTAAAAAGTA
1 TT-TTAAAAAGTG
35342084 TTTTGAAAAAGTG
1 TTTT-AAAAAGTG
* *
35342097 ATTTTGAAAAGTAC
1 -TTTTAAAAAGT-G
35342111 TTTTAAAAAGT
1 TTTTAAAAAGT
35342122 TTGATTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.10
13 33 0.80
14 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (12 bp):
TTTTAAAAAGTG
Found at i:35342095 original size:26 final size:26
Alignment explanation
Indices: 35342059--35342121 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
35342049 TTAACATTTT
*
35342059 TTTTAAGAAGTG-TTGTTAAAAAGTA-
1 TTTTAAAAAGTGATT-TTAAAAAGTAC
*
35342084 TTTTGAAAAAGTGATTTTGAAAAGTAC
1 TTTT-AAAAAGTGATTTTAAAAAGTAC
35342111 TTTTAAAAAGT
1 TTTTAAAAAGT
35342122 TTGATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 4 0.12
26 23 0.70
27 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (26 bp):
TTTTAAAAAGTGATTTTAAAAAGTAC
Found at i:35342100 original size:14 final size:13
Alignment explanation
Indices: 35342076--35342121 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
35342066 AAGTGTTGTT
35342076 AAAAAGTATTTTG
1 AAAAAGTATTTTG
35342089 AAAAAGTGATTTTG
1 AAAAAGT-ATTTTG
35342103 -AAAAGTACTTTT-
1 AAAAAGTA-TTTTG
35342115 AAAAAGT
1 AAAAAGT
35342122 TTGATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 23 0.77
14 6 0.20
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (13 bp):
AAAAAGTATTTTG
Found at i:35342520 original size:18 final size:18
Alignment explanation
Indices: 35342497--35342539 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
35342487 TTACTTATTT
35342497 AATATTATTTTTAT-TCAA
1 AATATT-TTTTTATATCAA
35342515 AATA-TTTTTTATATCAA
1 AATATTTTTTTATATCAA
35342532 ATATATTT
1 A-ATATTT
35342540 AAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 7 0.32
19 2 0.09
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTTTTTTATATCAA
Found at i:35342523 original size:16 final size:18
Alignment explanation
Indices: 35342504--35342539 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
35342494 TTTAATATTA
35342504 TTTTTAT-TCAAA-ATAT
1 TTTTTATATCAAATATAT
35342520 TTTTTATATCAAATATAT
1 TTTTTATATCAAATATAT
35342538 TT
1 TT
35342540 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTATATCAAATATAT
Found at i:35349290 original size:3 final size:3
Alignment explanation
Indices: 35349275--35349312 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
35349265 TCCCAATCTT
*
35349275 CAC CAC CAT CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
35349313 ACACAACTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.63, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:35350952 original size:23 final size:23
Alignment explanation
Indices: 35350905--35350952 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
35350895 GTATGAGATA
* **
35350905 AAAAAAACTCAAATATCAATTTG
1 AAAAAAACTCAAATACCAAACTG
*
35350928 AAAAAGACTCAAATACCAAACTG
1 AAAAAAACTCAAATACCAAACTG
35350951 AA
1 AA
35350953 TGTTTAAGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAAAAACTCAAATACCAAACTG
Found at i:35352024 original size:29 final size:30
Alignment explanation
Indices: 35351944--35352047 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
35351934 ATTAAATTAG
* * * *
35351944 AATTAAAATTTTAAATATACATTTAAACCAT-
1 AATTAAAA-TTTACATATATAATTACA-CATA
*
35351975 AATTAAAATTTTACGTATATAATTACACA-A
1 AATTAAAA-TTTACATATATAATTACACATA
*
35352005 AATTAAAATTTACATATATAATTACATATTA
1 AATTAAAATTTACATATATAATTACACA-TA
35352036 AATTAAAATTTA
1 AATTAAAATTTA
35352048 TGTATAATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 18 0.29
30 10 0.16
31 35 0.56
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (30 bp):
AATTAAAATTTACATATATAATTACACATA
Found at i:35352042 original size:31 final size:29
Alignment explanation
Indices: 35351975--35352047 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
35351965 TTTAAACCAT
*
35351975 AATTAAAATTTTACGTATATAATTACACAA
1 AATTAAAA-TTTACATATATAATTACACAA
*
35352005 AATTAAAATTTACATATATAATTACATATTA
1 AATTAAAATTTACATATATAATTACACA--A
35352036 AATTAAAATTTA
1 AATTAAAATTTA
35352048 TGTATAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 18 0.46
30 8 0.21
31 13 0.33
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (29 bp):
AATTAAAATTTACATATATAATTACACAA
Found at i:35361971 original size:47 final size:47
Alignment explanation
Indices: 35361902--35361996 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
35361892 CTAGGGCTAG
35361902 TAAAATAGTCAAGGATTCGATCCTTTCTTCTTTGTTCTTTTAGGTAT
1 TAAAATAGTCAAGGATTCGATCCTTTCTTCTTTGTTCTTTTAGGTAT
35361949 TAAAATAGTCAAGGATTCGATCCTTTCTTCTTTGTTCTTTTAGGTAT
1 TAAAATAGTCAAGGATTCGATCCTTTCTTCTTTGTTCTTTTAGGTAT
35361996 T
1 T
35361997 CATAGGAACG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (47 bp):
TAAAATAGTCAAGGATTCGATCCTTTCTTCTTTGTTCTTTTAGGTAT
Found at i:35364009 original size:3 final size:3
Alignment explanation
Indices: 35364001--35364036 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35363991 TTTCTCATGC
35364001 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35364037 GTACTCTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:35365410 original size:18 final size:21
Alignment explanation
Indices: 35365369--35365411 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
35365359 TATTTTTGTC
35365369 TAAACTTTCCTAAAATTCGAA
1 TAAACTTTCCTAAAATTCGAA
35365390 TAAACTTT-C-AAAATT-GAA
1 TAAACTTTCCTAAAATTCGAA
35365408 TAAA
1 TAAA
35365412 TAATCCAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 1 0.05
21 8 0.36
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (21 bp):
TAAACTTTCCTAAAATTCGAA
Found at i:35365741 original size:6 final size:6
Alignment explanation
Indices: 35365730--35365759 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35365720 GTTGGGTTAG
*
35365730 GTGCGA GTGCGA GTGCGA GTACGA GTGCGA
1 GTGCGA GTGCGA GTGCGA GTGCGA GTGCGA
35365760 CCGTATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.47, T:0.17
Consensus pattern (6 bp):
GTGCGA
Found at i:35365850 original size:12 final size:10
Alignment explanation
Indices: 35365820--35365846 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
35365810 TATGTTCTAT
35365820 AAAAAAATTC
1 AAAAAAATTC
35365830 AAAAAAATTC
1 AAAAAAATTC
35365840 AAAAAAA
1 AAAAAAA
35365847 AATTAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:35374013 original size:10 final size:10
Alignment explanation
Indices: 35374000--35374024 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35373990 TTTAAAATCA
35374000 TTTATAATAT
1 TTTATAATAT
35374010 TTTATAATAT
1 TTTATAATAT
35374020 TTTAT
1 TTTAT
35374025 CCGATGCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATAATAT
Found at i:35382651 original size:28 final size:28
Alignment explanation
Indices: 35382595--35382651 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
35382585 CTATAAAAAA
* *
35382595 TTATATTTGTAATAATTTTATATATTTT
1 TTATATTTGTAATAATTTCATATAATTT
*
35382623 TTATCATTT-TAATAATTTCATTTAATTT
1 TTAT-ATTTGTAATAATTTCATATAATTT
35382651 T
1 T
35382652 CTAGATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (28 bp):
TTATATTTGTAATAATTTCATATAATTT
Found at i:35382799 original size:38 final size:38
Alignment explanation
Indices: 35382721--35382804 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 38
35382711 TCATAATATA
* * * *
35382721 TCATAAATTTTGTAACTTTTTATATTCTTTTTGTAATTT
1 TCAT-AATTTTCTAACTTTTTATAATATTTTAGTAATTT
* *
35382760 TCTTAATTTTCTAACATTTTTATAATATTTTAGT-TTTT
1 TCATAATTTTCTAAC-TTTTTATAATATTTTAGTAATTT
35382798 TCATAAT
1 TCATAAT
35382805 ATATTAATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
38 19 0.51
39 18 0.49
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (38 bp):
TCATAATTTTCTAACTTTTTATAATATTTTAGTAATTT
Found at i:35382867 original size:16 final size:16
Alignment explanation
Indices: 35382846--35382887 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
35382836 TTTTATAAGC
35382846 TTTATAATTTCTA-ATT
1 TTTATAATTT-TATATT
35382862 TTTATATATTTTATATT
1 TTTATA-ATTTTATATT
35382879 TGTTATAAT
1 T-TTATAAT
35382888 ATTAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 8 0.35
17 10 0.43
18 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTATAATTTTATATT
Found at i:35389650 original size:167 final size:167
Alignment explanation
Indices: 35389372--35389710 Score: 651
Period size: 167 Copynumber: 2.0 Consensus size: 167
35389362 AAACGTTTCA
35389372 AAAAGTTGGTCTTCGAAATCCAGAGAAACAGGTTCGGGAGTCGGTTACGCATGAGGAAGGATTAG
1 AAAAGTTGGTCTTCGAAATCCAGAGAAACAGGTTCGGGAGTCGGTTACGCATGAGGAAGGATTAG
*
35389437 CACCCTCATACGCCCAGAATTGGTACCACATGATTATTTCCGGGTCTTATTTTATGAAAATAATG
66 CACCCTCATACGCCCAGAATTGGTACCACATGATTATTTCCGGGTCTTATTTTATGAAAACAATG
35389502 AAAACTCGAGTCAAGTTTAAAATGCGATATTTATTTT
131 AAAACTCGAGTCAAGTTTAAAATGCGATATTTATTTT
35389539 AAAAGTTGGTCTTCGAAATCCAGAGAAACAGGTTCGGGAGTCGGTTACGCATGAGGAAGGATTAG
1 AAAAGTTGGTCTTCGAAATCCAGAGAAACAGGTTCGGGAGTCGGTTACGCATGAGGAAGGATTAG
*
35389604 CACCCTCATACGCCCAGAATTGGTACCACATGATTATTTTCGGGTCTTATTTTATGAAAACAATG
66 CACCCTCATACGCCCAGAATTGGTACCACATGATTATTTCCGGGTCTTATTTTATGAAAACAATG
*
35389669 AAAACTCGAGTCAAGTTTAAAATGCGATGTTTATTTT
131 AAAACTCGAGTCAAGTTTAAAATGCGATATTTATTTT
35389706 AAAAG
1 AAAAG
35389711 GCTTTGTGCA
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 169 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (167 bp):
AAAAGTTGGTCTTCGAAATCCAGAGAAACAGGTTCGGGAGTCGGTTACGCATGAGGAAGGATTAG
CACCCTCATACGCCCAGAATTGGTACCACATGATTATTTCCGGGTCTTATTTTATGAAAACAATG
AAAACTCGAGTCAAGTTTAAAATGCGATATTTATTTT
Found at i:35390764 original size:59 final size:59
Alignment explanation
Indices: 35390682--35390944 Score: 370
Period size: 59 Copynumber: 4.5 Consensus size: 59
35390672 GGGAAAATTT
* * * *
35390682 GGGGTT-AAAATGGGATTTTGGAAAGCTCGGGGGTAAAATGATAATTTTTAGTGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATC
* *
35390740 GGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGATGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATC
** * *
35390799 GGGGTTAAAAAATGGAATTTTGGAAAGTTTAGGGGTAACACGGTAATTTTTGGTGAAA-C
1 GGGGTT-AAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATC
* *
35390858 TGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT-AAATGGTAATTTTGGGTGAAACC
1 -GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATC
*
35390917 GAGGTTAAAAATGGAATTTTGGAAAGTT
1 GGGGTTAAAAATGGAATTTTGGAAAGTT
35390945 TTTGGGTTAA
Statistics
Matches: 185, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
58 51 0.28
59 81 0.44
60 53 0.29
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (59 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATC
Found at i:35390820 original size:30 final size:29
Alignment explanation
Indices: 35390682--35390937 Score: 103
Period size: 30 Copynumber: 8.7 Consensus size: 29
35390672 GGGAAAATTT
*
35390682 GGGGTT-AAAATGGGATTTTG--GAAAGCTC
1 GGGGTTAAAAATGGAATTTTGATGAAA--TC
* * *
35390710 GGGGGT-AAAATGATAATTTTTAGTGAAATC
1 GGGGTTAAAAATG-GAATTTTGA-TGAAATC
*
35390740 GGGGTTAAAAATGGAATTTTG--GAAAGTTT
1 GGGGTTAAAAATGGAATTTTGATGAAA--TC
*
35390769 GGGGGT-AAAATGGTAATTTTTGATGAAATC
1 GGGGTTAAAAATGG-AA-TTTTGATGAAATC
*
35390799 GGGGTTAAAAAATGGAATTTTG--GAAAGTTTA
1 GGGGTT-AAAAATGGAATTTTGATGAAA---TC
* * *
35390830 GGGG-T-AACACGGTAATTTTTGGTGAAA-C
1 GGGGTTAAAAATGG-AA-TTTTGATGAAATC
35390858 TGGGGTTAAAAATGGAATTTTG--GAAAGTTC
1 -GGGGTTAAAAATGGAATTTTGATGAAA--TC
* * *
35390888 GGGGGT--AAATGGTAATTTTGGGTGAAACC
1 GGGGTTAAAAATGG-AATTTT-GATGAAATC
*
35390917 GAGGTTAAAAATGGAATTTTG
1 GGGGTTAAAAATGGAATTTTG
35390938 GAAAGTTTTT
Statistics
Matches: 175, Mismatches: 21, Indels: 63
0.68 0.08 0.24
Matches are distributed among these distances:
27 14 0.08
28 33 0.19
29 36 0.21
30 45 0.26
31 28 0.16
32 19 0.11
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (29 bp):
GGGGTTAAAAATGGAATTTTGATGAAATC
Found at i:35390825 original size:119 final size:117
Alignment explanation
Indices: 35390684--35390942 Score: 360
Period size: 119 Copynumber: 2.2 Consensus size: 117
35390674 GAAAATTTGG
* * *
35390684 GGTT-AAAATGGGATTTTGGAAAGCTCGGGGGTAAAATGATAATTTTTAGTGAAA-TCGGGGTTA
1 GGTTAAAAATGGAATTTTGGAAAGCTCAGGGGTAAAACGATAATTTTTAGTGAAACT-GGGGTTA
* * * *
35390747 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGATGAAATCGG
65 AAAATGGAATTTTGGAAAGTTCGGGGGT-AAATGGTAATTTTGGATGAAACCGA
* * * * *
35390801 GGTTAAAAAATGGAATTTTGGAAAGTTTAGGGGTAACACGGTAATTTTTGGTGAAACTGGGGTTA
1 GGTT-AAAAATGGAATTTTGGAAAGCTCAGGGGTAAAACGATAATTTTTAGTGAAACTGGGGTTA
*
35390866 AAAATGGAATTTTGGAAAGTTCGGGGGTAAATGGTAATTTTGGGTGAAACCGA
65 AAAATGGAATTTTGGAAAGTTCGGGGGTAAATGGTAATTTTGGATGAAACCGA
35390919 GGTTAAAAATGGAATTTTGGAAAG
1 GGTTAAAAATGGAATTTTGGAAAG
35390943 TTTTTGGGTT
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
117 24 0.19
118 25 0.20
119 76 0.60
120 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.31
Consensus pattern (117 bp):
GGTTAAAAATGGAATTTTGGAAAGCTCAGGGGTAAAACGATAATTTTTAGTGAAACTGGGGTTAA
AAATGGAATTTTGGAAAGTTCGGGGGTAAATGGTAATTTTGGATGAAACCGA
Found at i:35391551 original size:9 final size:9
Alignment explanation
Indices: 35391526--35391561 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
35391516 TCTTTTCTTT
35391526 TCTCTCTAAC
1 TCTCTC-AAC
35391536 TCTCTCAAC
1 TCTCTCAAC
*
35391545 TCCCTCAAC
1 TCTCTCAAC
35391554 TCTCTCAA
1 TCTCTCAA
35391562 AGCCGGCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.33
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:35392118 original size:3 final size:3
Alignment explanation
Indices: 35392112--35392145 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
35392102 TCTTCTTTTT
*
35392112 TTA TTA TTA TTAA TTA TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
35392146 ATAACACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:35392129 original size:10 final size:10
Alignment explanation
Indices: 35392114--35392142 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
35392104 TTCTTTTTTT
35392114 ATTATTATTA
1 ATTATTATTA
35392124 ATTATTATTA
1 ATTATTATTA
35392134 A-TATTATTA
1 ATTATTATTA
35392143 TTAATAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTATTATTA
Found at i:35392967 original size:6 final size:6
Alignment explanation
Indices: 35392958--35393051 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
35392948 TTGAATTTGA
* * *
35392958 TTAAAT TTAAAT CTAAA- ATAAAT TTAAAT AAGTAAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
** *
35393007 -TAAAT TTAAAT TTAAA- ACAAAT TTAAAA TT-AAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
35393052 AGCCCAAGCC
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
4 1 0.01
5 14 0.21
6 41 0.60
7 7 0.10
8 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:35392979 original size:17 final size:17
Alignment explanation
Indices: 35392959--35393038 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
35392949 TGAATTTGAT
*
35392959 TAAATTTAAATCTAAAA
1 TAAATTTAAATTTAAAA
*
35392976 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
*
35392990 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
35393007 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
35393024 CAAATTTAAAATTAA
1 TAAATTTAAATTTAA
35393039 TTTAAACTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.22
15 1 0.02
16 1 0.02
17 40 0.74
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:35392985 original size:11 final size:11
Alignment explanation
Indices: 35392965--35393044 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
35392955 TGATTAAATT
*
35392965 TAAATCTAAAA
1 TAAATTTAAAA
35392976 TAAATTTAAATAA
1 TAAATTT-AA-AA
*
35392989 GTAAATTTAAAT
1 -TAAATTTAAAA
* ** *
35393001 TTAAGATAAATT
1 TAAATTTAAA-A
35393013 TAAATTTAAAA
1 TAAATTTAAAA
*
35393024 CAAATTTAAAA
1 TAAATTTAAAA
*
35393035 TTAATTTAAA
1 TAAATTTAAA
35393045 CTTTAAAAGC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 31 0.58
12 11 0.21
13 4 0.08
14 7 0.13
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:35392994 original size:31 final size:31
Alignment explanation
Indices: 35392959--35393017 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
35392949 TGAATTTGAT
35392959 TAAATTTAAATCTAAAATAAATTTAAATAAG
1 TAAATTTAAATCTAAAATAAATTTAAATAAG
* *
35392990 TAAATTTAAATTTAAGATAAATTTAAAT
1 TAAATTTAAATCTAAAATAAATTTAAAT
35393018 TTAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAATTTAAATCTAAAATAAATTTAAATAAG
Found at i:35393040 original size:28 final size:29
Alignment explanation
Indices: 35392997--35393052 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
35392987 AAGTAAATTT
*
35392997 AAATTTAAGATAAATTTAAA-TTTAAAAC
1 AAATTTAAAATAAATTTAAACTTTAAAAC
*
35393025 AAATTTAAAATTAATTTAAACTTTAAAA
1 AAATTTAAAATAAATTTAAACTTTAAAA
35393053 GCCCAAGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATTTAAAATAAATTTAAACTTTAAAAC
Found at i:35415862 original size:18 final size:17
Alignment explanation
Indices: 35415812--35415862 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
35415802 AATTAATTTT
*
35415812 TTAAAATTTTGAAAATA
1 TTAAAATTTTCAAAATA
*
35415829 TTAGAA-TTTCAAAAAATA
1 TTAAAATTTTC--AAAATA
35415847 TTAAAATTATTCAAAA
1 TTAAAATT-TTCAAAA
35415863 GCATGAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 15 0.56
19 1 0.04
20 3 0.11
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (17 bp):
TTAAAATTTTCAAAATA
Found at i:35418410 original size:10 final size:10
Alignment explanation
Indices: 35418395--35418419 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35418385 TAATAATACA
35418395 AAAAAAATAT
1 AAAAAAATAT
35418405 AAAAAAATAT
1 AAAAAAATAT
35418415 AAAAA
1 AAAAA
35418420 TACTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:35420405 original size:18 final size:18
Alignment explanation
Indices: 35420373--35420408 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35420363 AGGGAGTATT
**
35420373 TTAATTAGATTGATTAAA
1 TTAATTAGAGGGATTAAA
35420391 TTAATTAGAGGGATTAAA
1 TTAATTAGAGGGATTAAA
35420409 ACAGGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (18 bp):
TTAATTAGAGGGATTAAA
Found at i:35426630 original size:31 final size:31
Alignment explanation
Indices: 35426595--35426665 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
35426585 ATATTTTATT
*
35426595 TAAAATATTATAGT-TTTTATA-ATTACATTCA
1 TAAAATATTA-AGTCTTTTA-ACAATACATTCA
*
35426626 TAAAA-ATTAAGTCTTTTAACAATACATTTA
1 TAAAATATTAAGTCTTTTAACAATACATTCA
35426656 TAAAAT-TTAA
1 TAAAATATTAA
35426666 TTATTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 4 0.11
30 26 0.74
31 5 0.14
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (31 bp):
TAAAATATTAAGTCTTTTAACAATACATTCA
Found at i:35426643 original size:30 final size:30
Alignment explanation
Indices: 35426595--35426674 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 30
35426585 ATATTTTATT
*
35426595 TAAAATATTATAGTTTTTATA-ATTACATTCA
1 TAAAA-ATTA-AGTTTTTATACAATACATTCA
*
35426626 TAAAAATTAAGTCTTTTA-ACAATACATTTA
1 TAAAAATTAAGT-TTTTATACAATACATTCA
* *
35426656 TAAAATTTAATTATTTTAT
1 TAAAAATTAAGT-TTTTAT
35426675 TTATAAATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
29 4 0.10
30 32 0.78
31 5 0.12
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (30 bp):
TAAAAATTAAGTTTTTATACAATACATTCA
Found at i:35429508 original size:26 final size:27
Alignment explanation
Indices: 35429461--35429523 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
35429451 TTTAATTTAT
* *
35429461 TAATTAAATAATATTTATTTTGA-AAA
1 TAATAAAATAATATTTAGTTTGATAAA
*
35429487 TAA-AAAATAAATATTTGGTTTGATTAAA
1 TAATAAAAT-AATATTTAGTTTGA-TAAA
35429515 TAATAAAAT
1 TAATAAAAT
35429524 GTCAAGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 15 0.50
28 6 0.20
29 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (27 bp):
TAATAAAATAATATTTAGTTTGATAAA
Found at i:35436057 original size:29 final size:29
Alignment explanation
Indices: 35435974--35436087 Score: 147
Period size: 29 Copynumber: 3.9 Consensus size: 29
35435964 CTCAAGAGGT
* * *
35435974 CCCTAATCTTTTCTAAAATTATATATAAC
1 CCCTAAACTTTTCTAAAATTACATTTAAC
* * * *
35436003 CCCCAAACCTTTCTAAAATCATATTTAAC
1 CCCTAAACTTTTCTAAAATTACATTTAAC
35436032 CCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCCTAAACTTTTCTAAAATTACA-TTTAAC
*
35436062 CCCTAAACTTTTCCAAAATTACATTT
1 CCCTAAACTTTTCTAAAATTACATTT
35436088 TGACCCCCGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 46 0.62
30 28 0.38
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTCTAAAATTACATTTAAC
Found at i:35436062 original size:30 final size:30
Alignment explanation
Indices: 35435974--35436094 Score: 149
Period size: 30 Copynumber: 4.1 Consensus size: 30
35435964 CTCAAGAGGT
* * *
35435974 CCCTAATCTTTTCTAAAATTATA-TATAAC
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* *
35436003 CCCCAAACCTTTCTAAAA-T-CATATTTAAC
1 CCCTAAACTTTTCTAAAATTACAT-TTTAAC
35436032 CCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* *
35436062 CCCTAAACTTTTCCAAAATTACATTTTGAC
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
35436092 CCC
1 CCC
35436095 CGAGCTTCTC
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 36 0.46
30 38 0.48
31 3 0.04
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (30 bp):
CCCTAAACTTTTCTAAAATTACATTTTAAC
Found at i:35436107 original size:30 final size:30
Alignment explanation
Indices: 35436046--35436183 Score: 127
Period size: 30 Copynumber: 4.6 Consensus size: 30
35436036 AAACTTTTCT
* ** * *
35436046 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCCGAGCTTCTCC
35436076 AAAATTACATTTTGACCCCCGAGCTTCTCC
1 AAAATTACATTTTGACCCCCGAGCTTCTCC
* * *
35436106 AAAATCACATTTTGACCCTCGAGCTTCTCT
1 AAAATTACATTTTGACCCCCGAGCTTCTCC
* * *
35436136 AAAATTTCATTTTCA-TCCCGAG-TTCTCC
1 AAAATTACATTTTGACCCCCGAGCTTCTCC
* * *
35436164 GAAACTCCATTTTTGACCCC
1 AAAATTACA-TTTTGACCCC
35436184 GTTTGTTTTT
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
28 11 0.13
29 10 0.11
30 66 0.76
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCCGAGCTTCTCC
Found at i:35438739 original size:20 final size:22
Alignment explanation
Indices: 35438711--35438760 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
35438701 CCACGTTAGC
*
35438711 AAATGATTTTAAAATT-A-TTA
1 AAATTATTTTAAAATTAATTTA
35438731 AAATTATTTTAAAATTAATTTA
1 AAATTATTTTAAAATTAATTTA
35438753 AAATTATT
1 AAATTATT
35438761 AAATAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 15 0.56
21 1 0.04
22 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AAATTATTTTAAAATTAATTTA
Found at i:35438742 original size:11 final size:11
Alignment explanation
Indices: 35438711--35438760 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
35438701 CCACGTTAGC
*
35438711 AAATGATTTTA
1 AAATTATTTTA
35438722 AAATTA--TTA
1 AAATTATTTTA
35438731 AAATTATTTTA
1 AAATTATTTTA
*
35438742 AAATTAATTTA
1 AAATTATTTTA
35438753 AAATTATT
1 AAATTATT
35438761 AAATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.26
11 25 0.74
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:35438772 original size:30 final size:32
Alignment explanation
Indices: 35438718--35438782 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
35438708 AGCAAATGAT
*
35438718 TTTAAAATTATTAAAATTATTTTAAAATT-AA
1 TTTAAAATTATTAAAATAATTTTAAAATTCAA
*
35438749 TTTAAAATTATT-AAATAATTTTAAATTTCAA
1 TTTAAAATTATTAAAATAATTTTAAAATTCAA
35438780 TTT
1 TTT
35438783 CATCTTCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAAAATTATTAAAATAATTTTAAAATTCAA
Found at i:35439052 original size:99 final size:99
Alignment explanation
Indices: 35438916--35439113 Score: 288
Period size: 99 Copynumber: 2.0 Consensus size: 99
35438906 ATTTGAACCA
* * * *
35438916 AACCATGGCTACTTCTCCACTTGAATTCTGAACCAAACCGTGGCTTCTTCTTCTTCCATCGCTCT
1 AACCATGGCTACTTCTCCACTTAAATTCTGAACCAAACCATGACTTCTTCTTCTTCCATCACTCT
* * * *
35438981 CCCAACCCTTCAAGGTTTTCTATTTTAATCTCAT
66 CCCAACACTTCAAGATTCTCTATTTCAATCTCAT
* *
35439015 AACCATGGCTACTTCTCCACTTAAATTTTGAATCAAACCATGACTTCTTCTTCTTCCATCACTCT
1 AACCATGGCTACTTCTCCACTTAAATTCTGAACCAAACCATGACTTCTTCTTCTTCCATCACTCT
**
35439080 CTTAACACTTCAAGATTCTCTATTTCAATCTCAT
66 CCCAACACTTCAAGATTCTCTATTTCAATCTCAT
35439114 TTATTAGGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.37
Consensus pattern (99 bp):
AACCATGGCTACTTCTCCACTTAAATTCTGAACCAAACCATGACTTCTTCTTCTTCCATCACTCT
CCCAACACTTCAAGATTCTCTATTTCAATCTCAT
Found at i:35445930 original size:8 final size:8
Alignment explanation
Indices: 35445917--35445942 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
35445907 TTTTGATAAC
35445917 ATTTTTAT
1 ATTTTTAT
35445925 ATTTTTAT
1 ATTTTTAT
35445933 ATTTTTAT
1 ATTTTTAT
35445941 AT
1 AT
35445943 AATCTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTAT
Found at i:35449934 original size:66 final size:66
Alignment explanation
Indices: 35449828--35449959 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
35449818 GGATGGATAT
*
35449828 CATCTTTACACATGCGAATGGTAACTGCTTTAAATTACAGTCAAATTTAACCAATTCAAGCAAGG
1 CATCTTTACACATGCGAATGGTAACTGCTTTAAATTACAGTCAAACTTAACCAATTCAAGCAAGG
35449893 A
66 A
35449894 CATCTTTACACATGCGAATGGTAACTGCTTTAAATTACAGTCAAACTTAACCAATTCAAGCAAGG
1 CATCTTTACACATGCGAATGGTAACTGCTTTAAATTACAGTCAAACTTAACCAATTCAAGCAAGG
35449959 A
66 A
35449960 TGTGATGTCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (66 bp):
CATCTTTACACATGCGAATGGTAACTGCTTTAAATTACAGTCAAACTTAACCAATTCAAGCAAGG
A
Found at i:35452281 original size:23 final size:23
Alignment explanation
Indices: 35452211--35452404 Score: 180
Period size: 23 Copynumber: 8.3 Consensus size: 23
35452201 ACGGAACAAG
* *
35452211 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
35452232 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
35452257 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
35452280 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
35452303 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
35452326 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
35452349 CAGAAAGCACACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
35452374 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
35452397 CAGAGAGC
1 CAGAGAGC
35452405 GCGCTAGTGT
Statistics
Matches: 145, Mismatches: 19, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
21 15 0.10
23 93 0.64
24 2 0.01
25 28 0.19
26 7 0.05
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:35452330 original size:69 final size:68
Alignment explanation
Indices: 35452211--35452404 Score: 205
Period size: 69 Copynumber: 2.8 Consensus size: 68
35452201 ACGGAACAAG
* *
35452211 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGT
35452274 GCTAAA
63 GCTAAA
35452280 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
35452344 CTAAT
64 CTAAA
* * * * * * *
35452349 CAGAAAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 CAGAGAGTACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAACAGAGAGC
35452405 GCGCTAGTGT
Statistics
Matches: 108, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
68 2 0.02
69 50 0.46
70 11 0.10
71 35 0.32
72 10 0.09
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (68 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCT
AAA
Found at i:35454573 original size:42 final size:42
Alignment explanation
Indices: 35454514--35454597 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
35454504 AAAAGAAATA
35454514 ACCTTTCAACACTTTGTTTTCTTTTCTTTTTCTCTCATTTTC
1 ACCTTTCAACACTTTGTTTTCTTTTCTTTTTCTCTCATTTTC
35454556 ACCTTTCAACACTTTGTTTTCTTTTCTTTTTCTCTCATTTTC
1 ACCTTTCAACACTTTGTTTTCTTTTCTTTTTCTCTCATTTTC
35454598 TTACTTTCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.12, C:0.26, G:0.02, T:0.60
Consensus pattern (42 bp):
ACCTTTCAACACTTTGTTTTCTTTTCTTTTTCTCTCATTTTC
Found at i:35463130 original size:2 final size:2
Alignment explanation
Indices: 35463125--35463190 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
35463115 TCAAAAATTA
35463125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35463167 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
35463191 TGTTCTTTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35469761 original size:3 final size:3
Alignment explanation
Indices: 35469753--35469783 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35469743 ATTTGGAAAT
35469753 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
35469784 TTATGTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35474249 original size:21 final size:21
Alignment explanation
Indices: 35474209--35474249 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35474199 GTCGCTTTAA
*
35474209 AAATATTTGTATAATTTTTTG
1 AAATATTTATATAATTTTTTG
* *
35474230 AAATTTTTATATATTTTTTT
1 AAATATTTATATAATTTTTT
35474250 AAGAAGAGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
AAATATTTATATAATTTTTTG
Found at i:35476619 original size:20 final size:20
Alignment explanation
Indices: 35476581--35476619 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35476571 TTTATTGCAT
*
35476581 TTTATAATTTTTTTTAATTA
1 TTTATAATTTTTTTGAATTA
35476601 TTTAT-ATTTTATTTGAATT
1 TTTATAATTTT-TTTGAATT
35476620 TTATTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTATAATTTTTTTGAATTA
Found at i:35484903 original size:59 final size:59
Alignment explanation
Indices: 35484828--35485011 Score: 167
Period size: 59 Copynumber: 3.1 Consensus size: 59
35484818 GAAAATGATA
* *
35484828 TTTTAGACATCCGAGGGTTAAACGGCAATTTTTAGAAA-AA-TCGAGATTAAAAACGAAAT
1 TTTTGGACATCCGAGGGTAAAACGGCAA-TTTTAGAAAGAATTCG-GATTAAAAACGAAAT
* * * * * *
35484887 TTTTGGACATCTGAGGGTAAAATGGTAATTTTGGAAAGAATTCGGATTAAAAATGGAAT
1 TTTTGGACATCCGAGGGTAAAACGGCAATTTTAGAAAGAATTCGGATTAAAAACGAAAT
* * * * * * * * *
35484946 TTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAGAA-TCGGGGTTAAAAATGGAAT
1 TTTTGGACATCCGAGGGTAAAACGGCAATTTTAGAAAGAATTC-GGATTAAAAACGAAAT
35485005 TTTTGGA
1 TTTTGGA
35485012 ATTTGGGGGT
Statistics
Matches: 109, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
58 10 0.09
59 96 0.88
60 3 0.03
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (59 bp):
TTTTGGACATCCGAGGGTAAAACGGCAATTTTAGAAAGAATTCGGATTAAAAACGAAAT
Found at i:35484942 original size:31 final size:32
Alignment explanation
Indices: 35484905--35485066 Score: 127
Period size: 28 Copynumber: 5.4 Consensus size: 32
35484895 ATCTGAGGGT
*
35484905 AAAATGGTAA-TTTTGGAAAGAATTC-GGATTA
1 AAAATGG-AATTTTTGGAAAGAATTCGGGGTTA
* *
35484936 AAAATGGAATTTTTGG--A-CATTCGGGGGT-
1 AAAATGGAATTTTTGGAAAGAATTCGGGGTTA
*
35484964 AAAATGGTAA-TTTTGGGAAGAA-TCGGGGTTA
1 AAAATGG-AATTTTTGGAAAGAATTCGGGGTTA
* *
35484995 AAAATGGAATTTTT-G---GAATTTGGGGGTA
1 AAAATGGAATTTTTGGAAAGAATTCGGGGTTA
** *
35485023 AAAATATAATTTTTGG-AAG-TTTCGGGGTTA
1 AAAATGGAATTTTTGGAAAGAATTCGGGGTTA
35485053 AAAATGGAATTTTT
1 AAAATGGAATTTTT
35485067 AAAAGTTTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.03
28 36 0.34
29 7 0.07
30 33 0.31
31 26 0.25
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (32 bp):
AAAATGGAATTTTTGGAAAGAATTCGGGGTTA
Found at i:35484967 original size:28 final size:28
Alignment explanation
Indices: 35484934--35485066 Score: 142
Period size: 30 Copynumber: 4.6 Consensus size: 28
35484924 GAATTCGGAT
35484934 TAAAAATGGAATTTTTGGACATTCGGGGG
1 TAAAAATGGAATTTTTGGA-ATTCGGGGG
* * *
35484963 T-AAAATGGTAATTTTGGGAAGAATCGGGGT
1 TAAAAATGG-AATTTTTGG-A-ATTCGGGGG
*
35484993 TAAAAATGGAATTTTTGGAATTTGGGGG
1 TAAAAATGGAATTTTTGGAATTCGGGGG
** *
35485021 TAAAAATATAATTTTTGGAAGTTTCGGGGT
1 TAAAAATGGAATTTTTGGAA--TTCGGGGG
35485051 TAAAAATGGAATTTTT
1 TAAAAATGGAATTTTT
35485067 AAAAGTTTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
28 31 0.36
29 10 0.12
30 37 0.44
31 7 0.08
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAATTCGGGGG
Found at i:35485027 original size:59 final size:59
Alignment explanation
Indices: 35484874--35485066 Score: 248
Period size: 59 Copynumber: 3.3 Consensus size: 59
35484864 AAAATCGAGA
* * * * * *
35484874 TTAAAAACGAAATTTTTGGACATCTGAGGGTAAAATGGTAATTTTGGAAAGAATTC-GGA
1 TTAAAAATGGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTGGGAAGAA-TCGGGG
*
35484933 TTAAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAGAATCGGGG
1 TTAAAAATGGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTGGGAAGAATCGGGG
* * **
35484992 TTAAAAATGGAATTTTTGGA-ATTTGGGGGTAAAAAT-ATAATTTTTGGAAGTTTCGGGG
1 TTAAAAATGGAATTTTTGGACATTTGGGGGT-AAAATGGTAATTTTGGGAAGAATCGGGG
35485050 TTAAAAATGGAATTTTT
1 TTAAAAATGGAATTTTT
35485067 AAAAGTTTAA
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
58 46 0.38
59 74 0.62
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
TTAAAAATGGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTGGGAAGAATCGGGG
Found at i:35485073 original size:30 final size:30
Alignment explanation
Indices: 35484986--35485144 Score: 137
Period size: 29 Copynumber: 5.4 Consensus size: 30
35484976 TTGGGAAGAA
* *
35484986 TCGGGGTTAAAAATGGAATTTTTGGAA-TT
1 TCGGGGTTAAAAATAGAATTTTTGAAAGTT
* * *
35485015 T-GGGGGTAAAAATATAATTTTTGGAAGTT
1 TCGGGGTTAAAAATAGAATTTTTGAAAGTT
* *
35485044 TCGGGGTTAAAAATGGAATTTTTAAAAGTT
1 TCGGGGTTAAAAATAGAATTTTTGAAAGTT
** *
35485074 TAAGGG-TAAAAATATAATTTTTGAAAGTT
1 TCGGGGTTAAAAATAGAATTTTTGAAAGTT
** * *
35485103 TTAGGGTT-AAAATATAATTTTGGAGAAGTT
1 TCGGGGTTAAAAATAGAATTTTTGA-AAGTT
* *
35485133 TGGGGGTCAAAA
1 TCGGGGTTAAAA
35485145 TATGATTTTT
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
28 22 0.21
29 44 0.41
30 38 0.36
31 3 0.03
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
TCGGGGTTAAAAATAGAATTTTTGAAAGTT
Found at i:35485132 original size:59 final size:58
Alignment explanation
Indices: 35485018--35485167 Score: 160
Period size: 59 Copynumber: 2.6 Consensus size: 58
35485008 TGGAATTTGG
* ** *
35485018 GGGTAAAAATATAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTAAAAGTTTAA
1 GGGTAAAAATATAATTTTTGAAAGTTTTAGGGTTAAAAAT-GAATTTTGAAAAGTTTAA
* **
35485077 GGGTAAAAATATAATTTTTGAAAGTTTTAGGGTTAAAATAT-AATTTTGGAGAAGTTTGG
1 GGGTAAAAATATAATTTTTGAAAGTTTTAGGGTTAAAA-ATGAATTTT-GAAAAGTTTAA
* * *
35485136 GGGTCAAAATATGATTTTTAGACAG-TTTAGGG
1 GGGTAAAAATATAATTTTT-GAAAGTTTTAGGG
35485168 ACCCTCAGGG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 6 0.08
59 66 0.85
60 6 0.08
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (58 bp):
GGGTAAAAATATAATTTTTGAAAGTTTTAGGGTTAAAAATGAATTTTGAAAAGTTTAA
Found at i:35485145 original size:30 final size:30
Alignment explanation
Indices: 35484988--35485163 Score: 157
Period size: 30 Copynumber: 6.0 Consensus size: 30
35484978 GGGAAGAATC
* **
35484988 GGGGTTAAAAATGGAATTTTTG-GAA-TTT
1 GGGGGTAAAAATATAATTTTTGAGAAGTTT
35485016 GGGGGTAAAAATATAATTTTTG-GAAGTTT
1 GGGGGTAAAAATATAATTTTTGAGAAGTTT
* ** *
35485045 CGGGGTTAAAAATGGAATTTTT-AAAAGTTT
1 -GGGGGTAAAAATATAATTTTTGAGAAGTTT
**
35485075 AAGGGTAAAAATATAATTTTTGA-AAGTTT
1 GGGGGTAAAAATATAATTTTTGAGAAGTTT
** * *
35485104 TAGGGTTAAAATATAATTTTGGAGAAGTTT
1 GGGGGTAAAAATATAATTTTTGAGAAGTTT
* *
35485134 GGGGGTCAAAATATGATTTTT-AGACAGTTT
1 GGGGGTAAAAATATAATTTTTGAGA-AGTTT
35485164 AGGGACCCTC
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
28 22 0.18
29 48 0.39
30 52 0.43
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGGGTAAAAATATAATTTTTGAGAAGTTT
Found at i:35487041 original size:6 final size:6
Alignment explanation
Indices: 35487030--35487084 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
35487020 TGCAATAATA
* *
35487030 TTAAAT TTAAA- TTAAAT TCAAAC TTAAA- TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
35487075 ATAAAT TTAA
1 TTAAAT TTAA
35487085 TTTCAGAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 14 0.34
6 27 0.66
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:35487045 original size:11 final size:11
Alignment explanation
Indices: 35487029--35487084 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
35487019 TTGCAATAAT
35487029 ATTAAATTTAA
1 ATTAAATTTAA
*
35487040 ATTAAATTCAA
1 ATTAAATTTAA
35487051 ACTTAAA-TTAA
1 A-TTAAATTTAA
35487062 ATTTAAATTTAA
1 A-TTAAATTTAA
*
35487074 AATAAATTTAA
1 ATTAAATTTAA
35487085 TTTCAGAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 29 0.74
12 10 0.26
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:35487046 original size:5 final size:5
Alignment explanation
Indices: 35487029--35487086 Score: 53
Period size: 5 Copynumber: 10.6 Consensus size: 5
35487019 TTGCAATAAT
*
35487029 ATTAA ATTTAA ATTAA ATTCAA ACTTAA ATTAA ATTTAA ATTTAA AATAA
1 ATTAA A-TTAA ATTAA ATT-AA A-TTAA ATTAA A-TTAA A-TTAA ATTAA
*
35487079 ATTTA ATT
1 ATTAA ATT
35487087 TCAGAACAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
5 22 0.48
6 22 0.48
7 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:35487082 original size:17 final size:17
Alignment explanation
Indices: 35487030--35487084 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
35487020 TGCAATAATA
35487030 TTAAATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
* *
35487047 TCAAACTTAAATTAAAT
1 TTAAATTTAAATTAAAT
*
35487064 TTAAATTTAAAATAAAT
1 TTAAATTTAAATTAAAT
35487081 TTAA
1 TTAA
35487085 TTTCAGAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:35489464 original size:15 final size:14
Alignment explanation
Indices: 35489441--35489491 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
35489431 TGTGAAAGTT
35489441 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
35489455 TTTTATAAAATAAAA
1 TTTTA-AAAATAAAA
*
35489470 TCTTAAAAATAATTAA
1 TTTTAAAAATAA--AA
35489486 TTTTAA
1 TTTTAA
35489492 TAACGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:35490652 original size:14 final size:14
Alignment explanation
Indices: 35490633--35490690 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
35490623 TGAATGTTTG
35490633 CATGACATAGTATA
1 CATGACATAGTATA
35490647 CATGACATAG-ATA
1 CATGACATAGTATA
** * *
35490660 TTTGA-AT-GTTTG
1 CATGACATAGTATA
*
35490672 CATAACATAGTATA
1 CATGACATAGTATA
35490686 CATGA
1 CATGA
35490691 GACTTCTTAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
11 1 0.03
12 5 0.16
13 8 0.26
14 17 0.55
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (14 bp):
CATGACATAGTATA
Found at i:35493774 original size:23 final size:22
Alignment explanation
Indices: 35493745--35493787 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
35493735 TTTAGCATTT
*
35493745 ATATATATTTTTAAATATTTTTA
1 ATATATATTTATAAA-ATTTTTA
35493768 ATATATATTTATAAAATTTT
1 ATATATATTTATAAAATTTT
35493788 GGAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATATATTTATAAAATTTTTA
Found at i:35496767 original size:22 final size:22
Alignment explanation
Indices: 35496742--35496787 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35496732 TCAATCATAA
*
35496742 ATAAAAAAATAATTAA-AGATTT
1 ATAAAAAAAT-ATTAATAAATTT
*
35496764 ATAAATAAATATTAATAAATTT
1 ATAAAAAAATATTAATAAATTT
35496786 AT
1 AT
35496788 TTAAACCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAAAAAAATATTAATAAATTT
Found at i:35499345 original size:3 final size:3
Alignment explanation
Indices: 35499337--35499361 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35499327 TTTTGCCACC
35499337 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
35499362 TTATGTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:35509474 original size:30 final size:31
Alignment explanation
Indices: 35509440--35509499 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
35509430 AACAACCCAT
*
35509440 TGACTTAAAT-AAAAATTTTGAATAGTTTAG
1 TGACTTAAATGAAAAATTTTGAATAATTTAG
*
35509470 TGACTTAAATGAAAACTTTTGAATAATTTA
1 TGACTTAAATGAAAAATTTTGAATAATTTA
35509500 ATAATCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (31 bp):
TGACTTAAATGAAAAATTTTGAATAATTTAG
Found at i:35515201 original size:22 final size:23
Alignment explanation
Indices: 35515162--35515206 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
35515152 AAGATTTATA
*
35515162 ATTTTTAGTGATTCATTTAGTAAT
1 ATTTTTAGT-ATTAATTTAGTAAT
*
35515186 ATTTTTAGT-TTAATTTGGTAA
1 ATTTTTAGTATTAATTTAGTAA
35515207 ATCAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (23 bp):
ATTTTTAGTATTAATTTAGTAAT
Found at i:35516186 original size:32 final size:32
Alignment explanation
Indices: 35516150--35516246 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 32
35516140 AGGATGACAC
* *
35516150 GTACCAACTAGATACTTTTTGGACAAGTTCAT
1 GTACCAACTAGATACTTTTTGAACAAGTTCAA
* *
35516182 GTACCAACTAAATATTTTTTTGAACAAGTTCAA
1 GTACCAACTAGATA-CTTTTTGAACAAGTTCAA
* *
35516215 GTATCAACTAGATAC-TTTTGAATAAGTTCAA
1 GTACCAACTAGATACTTTTTGAACAAGTTCAA
35516246 G
1 G
35516247 AGACAAACTA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 16 0.29
32 13 0.23
33 27 0.48
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (32 bp):
GTACCAACTAGATACTTTTTGAACAAGTTCAA
Found at i:35517104 original size:16 final size:16
Alignment explanation
Indices: 35517065--35517104 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
35517055 ATAGCCATTC
35517065 TTAGTTTTATTTTGTT
1 TTAGTTTTATTTTGTT
35517081 TTATGTTTTATTTT-TT
1 TTA-GTTTTATTTTGTT
35517097 TTGAGTTT
1 TT-AGTTT
35517105 CTAAAGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.75
Consensus pattern (16 bp):
TTAGTTTTATTTTGTT
Found at i:35521031 original size:23 final size:23
Alignment explanation
Indices: 35521005--35521050 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35520995 TGGAAATCCA
35521005 GTTTTTCCCTCTTCTCAGTTTAC
1 GTTTTTCCCTCTTCTCAGTTTAC
35521028 GTTTTTCCCTCTTCTCAGTTTAC
1 GTTTTTCCCTCTTCTCAGTTTAC
35521051 TGTTAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.30, G:0.09, T:0.52
Consensus pattern (23 bp):
GTTTTTCCCTCTTCTCAGTTTAC
Found at i:35526663 original size:22 final size:23
Alignment explanation
Indices: 35526625--35526667 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
35526615 CGAATAGTTC
*
35526625 AATAATTTTAATGAAAATTTTTG
1 AATAATTTTAATAAAAATTTTTG
35526648 AATAA-TTTAATAAAAATTTT
1 AATAATTTTAATAAAAATTTT
35526668 GTAACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAAAAATTTTTG
Found at i:35532582 original size:2 final size:2
Alignment explanation
Indices: 35532570--35532612 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
35532560 TTCTTGCATA
35532570 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35532610 AT A
1 AT A
35532613 ATTAAATACC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.